Thalassiosira pseudonana CCMP1335 chromosome 9, whole genome shotgun sequence.
Eukaryota; Stramenopiles; Bacillariophyta; Coscinodiscophyceae; Thalassiosirophycidae; Thalassiosirales; Thalassiosiraceae; Thalassiosira.
The Phaeodactylum genome reveals the evolutionary history of diatom genomes
The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism
Submitted (15-JUN-2017) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA
Submitted (18-SEP-2008) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
PROVISIONAL REFSEQ: This record has not yet been subject to final\nNCBI review. The reference sequence is identical to CM000645.\nURL -- http://www.jgi.doe.gov/thalassiosira\nJGI Project ID: 2662235\nContacts: E. Virginia Armbrust (armbrust@u.washington.edu)\n Igor Grigoriev (ivgrigoriev@lbl.gov)\nThe clone of P. pseudonana that was sequenced is CCMP1335 and is\navailable from the Center for Culture of Marine Phytoplankton\n(http://ccmp.bigelow.org). This clone was collected in 1958 from\nMoriches Bay (Long Island, New York) and has been maintained\ncontinuously in culture.\nAnnotation was done by the JGI Annotation team and the Diatom\nConsortium.\nChromosomes 7 and 18 are complete and present in GenBank records\nCP001160 and CP001159, respectively.\nThe JGI and collaborators endorse the principles for the\ndistribution and use of large scale sequencing data adopted by the\nlarger genome sequencing community and urge users of this data to\nfollow them. It is our intention to publish the work of this\nproject in a timely fashion and we welcome collaborative\ninteraction on the project and analysis.\n(http://www.genome.gov/page.cfm?pageID=10506376)\nAnnotated scaffolds were added in January 2009.\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: INSDC submitter\nAnnotation Status :: Full annotation\nAnnotation Pipeline :: Eukaryotic Annotation Propagation Pipeline\n##Genome-Annotation-Data-END##
based on presence of leucine-rich repeats, including rbonuclease inhibitor type; putative protein containing leucine-rich repeats, including those of ribonuclease inhibitor type
probably involved in protein degradation (from similarity), most similar to cyanobacterial counterparts. At least 6 more such genes are present in the T. pseudonana genome.; belongs to the clp-superfamily of proteases, chaperones, and heat shock proteins; regulatory subunit
similarity to cytochrome P450 monooxygenase; hypothetical protein
Supported by partial Phaeodactylum cDNA. Half of the gene has high similarity to several carboxylases (alpha subunit), most likely propionyl- or acetyl-CoA.; unknown carboxylase alpha chain
based on sequence similarity to Arabidopsis protein and presence of multiple domains found in excision repair enzymes
Putative protein with similarities to adenylate cyclase (ATP pyrophosphate-lyase) (Adenylyl cyclase), e.g. gi|1169151|sp|P08678|CYAA_YEAST Adenylate cyclase (model%: 74, hit%: 87, score: 289, %id: 4) [Saccharomyces cerevisiae]; putative protein with similarity to adenylate cyclase
strong EST support from T. pseudonana and P. tricornutum cDNAs; hypothetical protein with no known similarity
pathogenesis-related transcription factor
Putative pathogenesis-related transcription factor (AP2 domain); similar to gi|25354653|pir||C84686 probable AP2 domain transcription factor [imported] - Arabidopsis thaliana (model%: 100, hit%: 33, score: 149, %id: 30) [Arabidopsis thaliana]
platelet-activating factor acetylhydrolase beta subunit-like protein
contains conserved G-protein WD-40 repeats (IPR001680). strong alignment with PAF from other organisms (40% identity over 450 amino acids)
aligns well with protein with iron-sulfur cluster assembly,protein assembly. Found by searching for nif N fixation genes in Inter-Pro.Not picked up by KEGG.
Putative pathogenesis-related transcription factor (AP2 domain); similar to ath:At3g20310 MQC12.13; ethylene responsive element binding factor, putative (model%: 100, hit%: NO HIT LENGTH, score: 115, %id: 46) [Arabidopsis thaliana]
Putative pathogenesis-related transcription factor (AP2 domain); similar to ath:At2g28550 T17D12.11; putative AP2 domain transcription factor (model%: 100, hit%: NO HIT LENGTH, score: 149, %id: 31) [Arabidopsis thaliana]
Putative protein similar to polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) (PNPase) custom_KEGG (model%: 69, hit%: 88, score: 812, %id: 30) [Listeria innocua] and syn:sll1043 polyribonucleotide nucleotidyltransferase custom_KEGG (model%: 69, hit%: 91, score: 725, %id: 31) [Synechocystis sp. PCC 6803]; EST support; putative protein similar to polyribonucleotide nucleotidyltransferase
CTP + phosphatidate = diphosphate + CDP-diacylglycerol; cytidine-5'-diphosphate-diacylglycerol synthase
beta subunit of tetrameric clathrin adaptor complex AP1
clathrin adaptor protein complex 1 is involved in protein sorting in the trans-Golgi network and endosomes; APB1, AP1B1, BAM22, beta1-adaptin
zinc finger like protein, CXXC motif, DNA binding/transcription factor
PAS domains are involved in many signalling proteins where they are used as a signal sensor domain. PAS domains appear in archaea, bacteria and eukarya. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Heme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in: Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein.
hypothetical protein with weak similarity to nyd-sp28
based on sequence similarity to mammalian homologs and presence of defining domains
dolichyl pyrophosphate Glc1Man9GlcNAc2 alpha-1,3-glucosyltransferase
involved in N-glycan biosynthesis in the ERno EST data
One of four component proteins of the enzyme glycine decarboxylase. Together with serine hydroxymethyltransferase this complex catalyzes the formation of one serine from two glycine. This reaction is part of the photorespiratory pathway (glycolate metabolism) and occurs in the mitochondria.
Proteasome subunit beta (20S proteasome alpha subunit D) (20S proteasome subunit beta-4) (model%: 83, hit%: 82, score: 424, %id: 50) [Oryza sativa]
This gene model matches other conserved hypothetic proteins in bacteria and yeast.; conserved hypothetical protein
eukaryotic translation initiation factor 2 alpha subunit
addition to WINNIE annotation: N-terminus contains putative ER signal peptide predicted by SignalP (probability 0.963; cleavage site between pos. 15 and 16: CSA-FV). Putatively ER targeted. ER signal is followed by putative mitochondrial leader sequence predicted by targetP (probability 0.716; length 42 aa).; putative protein containing the motifs for prolyly 4-hydroxylase alpha subunit and 20G-Fe oxygenase superfamily
putative protein of unknown function containing a TRAF zinc-finger domain; putative protein of unknown function containing a TRAF zinc-finger domain
Hits to other unknown putative and hypothetical proteins from A. thaliana and S. pombe. The best hit was to At4g22990-68296.m02425 F7H19.170 a putative protein, hypothetical protein from A. thaliana with 31.88% (146/458) identity. It also had a hit to spo:SPCC330.07c an MFS efflux transporter of unknown specificity from S.pombe with 21.00% (92/438) identity.; putative protein similar to At4g22990-68296.m02425 F7H19.170
Has some similarity to alkaline phosphatase, putative transmembrane protein, putative secreted protein; unknown protein
I got to this gene under the Alanine and aspartate metobolism category in KEGG. Putative function: synthesizes histamine from histidine.
dolichyl pyrophosphate Glc1Man9GlcNAc2; Dolichyl-P-Glc:Man9GlcNAc2-PP-dolichyl glucosyltransferase
significant homology to human ALG8;ALG6, ALG8 glycosyltransferase family. N-linked (asparagine-linked) glycosylation of proteins is mediated by a highly conserved pathway in eukaryotes, in which a lipid (dolichol phosphate)-linked oligosaccharide is assembled at the endoplasmic reticulum membrane prior to the transfer of the oligosaccharide moiety to the target asparagine residues. This oligosaccharide is composed of Glc(3)Man(9)GlcNAc(2). The addition of the three glucose residues is the final series of steps in the synthesis of the oligosaccharide precursor. Alg6 transfers the first glucose residue, and Alg8 transfers the second one
Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both side by a twelve residue alpha-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand).
This model has no EST support yet. It contains the conserved domain for prolyl 4-hydroxylase alpha subunit. It is most similar other prolyl 4-hydroxylase alpha subunits from Arabidopsis thaliana.; hypothetical protein similar to prolyl 4-hydroxylase alpha subunit
Adenosine kinase (AK2) (Adenosine 5'-phosphotransferase 2), very similar to gi|17366963|sp|Q9LZG0|ADK2_ARATH Adenosine kinase 2 (AK 2)(model%: 100, hit%: 96, score: 935, %id: 54) [Arabidopsis thaliana]; EST support
Putative protein of unknown function with similarities to phospholipases, e.g. gi|21070604|gb|AAM34347.1| (AC117082) PUTATIVE PHOSPHOLIPASE [Dictyostelium discoideum] (model%: 91, hit%: 62, score: 271, %id: 28) [Dictyostelium discoideum]; putative protein of unknown function with similarity to phospholipases
histone acetyltransferase MOZ/SAS-type hat
Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases
Very distant and improbable similarity to various known sequences.; hypothetical gene
Possible phospholipid:diacylglycerol acyltransferase but not strong hit.; unknown protein
Good hits to other transporters especially transporters specific for acetylcholine and monoamine.; putative MFS transporter of unknown specificity
Protein phosphatase 2C (PP2C) is one of the four major classes of mammalian serine/threonine specific protein phosphatases; shows broad substrate specificity and is dependent on divalent cations; putative protein phosphatase
HSF6, Contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor; HSF6, contains heat shock transcription factor DNA-binding domain, DNA binding, transcription factor
calcium/proton exchanger, calcium antiporter
This is a group of calcium/proton exchanger proteins. In Arabidopsis the transporter is responsible for maintaining low cytosolic-free Ca2+ concentrations in the plant cells by catalyzing pH gradient-energized vacuolar Ca2+ accumulation.
T. weissflogii EST support and limited sequence similarity to other proteins of unknown function; putative protein of unknown function
This gene may be involved in lysine degradation. It is most similar to genes from mouse and human. There is some EST support for this gene.; hypothetical protein
heterotrimeric G protein alpha subunit 1
Guanine nucleotide binding proteins (G-proteins) are a family of membrane-associated proteins that couple extracellularly-activated integral-membrane receptors to intracellular effectors, such as ion channels and enzymes that vary the concentration of second messenger molecules. G-proteins are composed of 3 subunits (alpha, beta and gamma) which, in the resting state, associate as a trimer at the inner face of the plasma membrane. This family consists of the G protein alpha subunit which binds guanyl nucleotide and is a weak GTPase.
Putative protein of unknown function containing leucine-rich repeats, with some similarities to gi|7488988|pir||T30553 disease resistance protein Hcr2-5D - tomato (model%: 91, hit%: 28, score: 491, %id: 37) [Lycopersicon esculentum]; EST support; putative protein of unknown function containing leucine-rich repeats
based on sequence similarity to hypothetical proteins from metazoa; putative protein of unknown function
supported by EST data; hypothetical EF hand containing protein with similarity to rRNA processing enzyme
Identified based on sequence similarity. May be involved in detoxifying reactive electrophillic compounds by conjugating them to glutathione (based on InterPro description).
supported by EST data; EST support.; hypothetical protein with
Serine/threonine (S/T) phosphatases catalyse the dephosphorylation of phosphoserine and phosphothreonine residues; contains conserved serine/threonine phosphatase domain
EST support.; putative protein of unknown function with
mate efflux protein, multi antimicrobial extrusion family
These proteins are integral membrane proteins, previously of unknown function, but now thought to belong to the Multi Antimicrobial Extrusion (MATE) Family (TC 2.A.66). The MATE family consists of probable efflux proteins including a functionally characterized multi drug efflux system from Vibrio parahaemolyticus, a putative ethionine resistance protein of Saccharomyces cerevisiae, and the functionally uncharacterized DNA damage-inducible protein F (DinF) of E. coli. These proteins have 12 probable transmembrane regions. The pig Niemann-pick C1 protein is also a member of this family, and is involved in the intracellular trafficking of cholesterol.
based on sequence similarity to hypothetical proteins from metazoans; putative protein of unknown function
This family includes the mammalian type II renal Na+/Pi-cotransporters and other proteins from lower eukaryotes and bacteria some of which are also Na+/Pi-cotransporters. In the kidney these proteins may be involved in actively transporting phosphate into cells via Na+ cotransport in the renal brush border membrane
putative protein of unknown function supported by
hypothetical glutaminase, nitrogen metabolism
Excellent hits to ABC transporters, domains.
putative protein of unknown function supported by EST data
RS1, ribosomal protein 1, 40S small ribosomal subunit, nuclear, translation, protein biosynthesis
The H(+)-transporting two-sector ATPase is a component of the cytoplasmic membrane of eubacteria, the inner membrane of mitochondria, and the thylakoid membrane of chloroplasts. The ATPase complex is composed of an oligomeric transmembrane sector, called CF(0) which is composed of nine subunits, A, B, C, D, E, F, G, F6 and 8 (or A6L), and a catalytic core, called coupling factor CF(1). The former acts as a proton channel; the latter is composed of five subunits, alpha, beta, gamma, delta and epsilon.
Contains homology to protein kinase domains; putative protein kinase
similar to GS28_ARATH (28 kDa Golgi SNARE component)
Protein kinases comprise a large family of enzymes that mediate the response of eukaryotic cells to external stimuli by phosphorylation of hydroxyamino acids; putative protein kinase
putative protein kinase containing cyclic nucleotide-binding domain; putative protein kinase containing cyclic nucleotide-binding domain
hypothetical protein with formin homology
hypothetical protein with similarity to hypothetical protein from nostoc with putative ATP/GTP binding site
fucoxanthin chl a/c light-harvesting protein, lhcr type
Presumably cayalyzes the reation: S-adenosyl-L-methionine + 5alpha-cholesta-8,24-dien-3beta-ol = S-adenosyl-L-homocysteine + 24-methylene-5alpha-cholest-8-en-3beta-ol.
Adenosuccinate synthase (IMP-aspartate ligase) (ADSS) (AMPSase), very similar to gi|131641|sp|P21900|PURA_DICDI ADENYLOSUCCINATE SYNTHETASE (model%: 100, hit%: 96, score: 1164, %id: 52) [Dictyostelium discoideum]; EST support